Variant report

Variant	rs12511889
Chromosome Location	chr4:79222347-79222348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10008653	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10010118	0.81[TSI][hapmap]
rs1017649	0.80[CEU][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes]
rs10461146	0.92[AMR][1000 genomes]
rs12500443	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12501798	0.94[AMR][1000 genomes]
rs12502139	0.92[AMR][1000 genomes]
rs12502685	0.91[AMR][1000 genomes]
rs12504081	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12505633	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12505887	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12506036	0.91[AMR][1000 genomes]
rs12511360	0.92[AMR][1000 genomes]
rs12511808	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12641094	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13107378	0.92[AMR][1000 genomes]
rs13108102	0.92[AMR][1000 genomes]
rs13114110	0.90[AMR][1000 genomes]
rs13117388	0.80[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes]
rs13119684	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13136648	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13138795	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13144541	0.82[EUR][1000 genomes]
rs1454892	0.87[AMR][1000 genomes]
rs1454898	0.92[AMR][1000 genomes]
rs1484344	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17003028	0.88[CEU][hapmap]
rs17455826	0.80[CEU][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes]
rs1840391	0.94[AMR][1000 genomes]
rs1840392	0.93[AMR][1000 genomes]
rs2124143	0.89[AMR][1000 genomes]
rs2124144	0.86[AMR][1000 genomes]
rs2198635	0.93[AMR][1000 genomes]
rs28737438	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34535077	0.86[AMR][1000 genomes]
rs34595864	0.85[AMR][1000 genomes]
rs34643532	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35290872	0.92[AMR][1000 genomes]
rs35291597	0.94[AMR][1000 genomes]
rs35419939	0.93[AMR][1000 genomes]
rs35683023	0.88[AMR][1000 genomes]
rs35828300	0.94[AMR][1000 genomes]
rs41537644	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4515188	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859923	0.84[AMR][1000 genomes]
rs58101131	0.86[AMR][1000 genomes]
rs62309861	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62310017	0.94[AMR][1000 genomes]
rs62310021	0.81[AMR][1000 genomes]
rs62310023	0.94[AMR][1000 genomes]
rs62310045	0.93[AMR][1000 genomes]
rs6815945	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6854207	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6856362	0.93[AMR][1000 genomes]
rs7656032	0.91[AMR][1000 genomes]
rs7661907	0.91[EUR][1000 genomes]
rs7681247	0.88[AMR][1000 genomes]
rs7686297	0.89[AMR][1000 genomes]
rs7693120	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs943821	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs943822	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12511889	PARM1	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79198600-79241400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:79208400-79229200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:79208800-79236800	Weak transcription	Fetal Intestine Large	intestine
4	chr4:79214000-79223400	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:79215600-79223000	Weak transcription	Fetal Brain Male	brain
6	chr4:79215600-79229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:79215800-79237600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:79215800-79243800	Weak transcription	Right Ventricle	heart
9	chr4:79218000-79224600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:79218200-79222800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:79218600-79229200	Weak transcription	Fetal Stomach	stomach
12	chr4:79218600-79230000	Weak transcription	Fetal Kidney	kidney
13	chr4:79220000-79228200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:79220200-79223000	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr4:79220400-79246600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:79220400-79246600	Weak transcription	HMEC	breast
17	chr4:79220600-79222600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:79220600-79229800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:79220600-79234200	Weak transcription	HSMMtube	muscle
20	chr4:79220600-79241400	Weak transcription	Aorta	Aorta
21	chr4:79220800-79222800	Weak transcription	NHLF	lung
22	chr4:79220800-79228600	Weak transcription	Fetal Intestine Small	intestine
23	chr4:79220800-79243000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:79221000-79237400	Weak transcription	Fetal Heart	heart
25	chr4:79221000-79240000	Weak transcription	Psoas Muscle	Psoas
26	chr4:79221200-79228800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:79221200-79229000	Weak transcription	HepG2	liver
28	chr4:79221200-79229200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:79221200-79229800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:79221200-79229800	Weak transcription	Fetal Lung	lung
31	chr4:79221200-79231200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:79221200-79232600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr4:79221200-79263000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:79221400-79223000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:79221600-79228200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:79221800-79222600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:79221800-79229000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:79222000-79229000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:79222200-79229000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:79222200-79229200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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